PUBLICATIONS

2016

  • R Di Niro, O Snir, K Kaukinen, G Yaari, KEA Lundin, NT Gupta, SH Kleinstein, M Cols, A Cerutti, M Mäki, MJ Shlomchik, LM Sollid, Responsive population dynamics and wide seeding into the duodenal lamina propria of transglutaminase-2-specific plasma cells in celiac disease, Mucosal Immunology, 9, 254–264
  • Ruxandra Covacu, Hagit Philip, Merja Jaronen, Jorge Almeida, Jessica E. Kenison, Samuel Darko, Chun-Cheih Chao, Gur Yaari, Yoram Louzoun, Liran Carmel, Daniel C. Douek, Sol Efroni, and Francisco J. Quintana, System-wide Analysis of the T Cell Response, Cell Reports, doi: 10.1016/j.celrep.2016.02.056
  • Dror Hibsh, Kenneth H. Buetow, Gur Yaari, and Sol Efroni, Quantification of read species behavior within whole genome sequencing of cancer genomes for the stratification and visualization of genomic variation, Nucleic Acids Research, doi:10.1093/nar/gkw031

2015

  • Gur Yaari and Steven H. Kleinstein, Practical guidelines for B-cell receptor repertoire sequencing analysis, Genome Medicine, 7:121
  • Gur Yaari, Jennifer Benichou, Jason Vander Heiden, Steven H. Kleinstein and Yoram Louzoun, The mutation patterns in B-cell immunoglobulin receptors reflect the influence of selection acting at multiple time-scales, Philosophical Transactions B, 370: 20140242.
  • Namita T. Gupta, Jason Vander Heiden, Mohamed Uduman, Daniel Gadala-Maria, Gur Yaari, and Steven H. Kleinstein, Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data, Bioinformatics, doi:10.1093/bioinformatics/btv359
  • Omri Snir, Luka Mesin, Moriah Gidoni, Knut E. A. Lundin, Gur Yaari*, and Ludvig M. Sollid*, Analysis of Celiac Disease Autoreactive Gut Plasma Cells and Their Corresponding Memory Compartment in Peripheral Blood Using High-Throughput Sequencing, The Journal of Immunology, 194(12), 5703-5712
  • Yuval R. Zelnik, Sorin Solomon, and Gur Yaari Species survival emerge from rare events of individual migration, Scientific Reports 5, Article number:7877 doi:10.1038/srep07877.
  • Daniel Gadala-Maria, Gur Yaari, Mohamed Uduman, and Steven H. Kleinstein, Automated analysis of high-throughput B cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles, Proceedings of the National Academy of Sciences, 112(8), E862–E870

2014

  • Joel N. H. Stern*, Gur Yaari*, Jason A. Vander Heiden*, George Church, William F. Donahue, Rogier Q. Hintzen, Anita J. Huttner, Jon D. Laman, Rashed M. Nagra, Alyssa Nylander, David Pitt, Sriram Ramanan, Bilal A. Siddiqui, Francois Vigneault, Steven H. Kleinstein, David A. Hafler and Kevin C. O’Connor. Antibody repertoire sequencing demonstrates that B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes, Science Translational Medicine 6, 248ra107.
  • Uri Laserson, Francois Vigneault, Daniel Gadala-Maria, Gur Yaari, Mohamed Uduman, Jason A. Vander Heiden, William Kelton, Sang Taek Jung, Yi Liu, Jonathan Laserson, Raj Chari, Je-Hyuk Lee, Ido Bachelet, Brendan Hickey, Erez Lieberman-Aiden, Bozena Hanczaruk, Birgitte B. Simen, Michael Egholm, Daphne Koller, George Georgiou, Steven H. Kleinstein and George M. Church, High-resolution antibody dynamics of vaccine-induced immune responses, Proceedings of the National Academy of Sciences. 111(13):4928.
  • Jason A. Vander Heiden*, Gur Yaari*, Mohamed Uduman, Joel N.H. Stern, Kevin C. O’Connor, David A. Hafler, Francois Vigneault and Steven H. Kleinstein. pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires, Bioinformatics doi:10.1093/bioinformatics/btu138.

2013

  • Devin Sok, Uri Laserson, Jonathan Laserson, Yi Liu, Francois Vigneault, Jean-Philippe Julien, Bryan Briney, Alejandra Ramos, Karen F. Saye, Khoa Le, Alison Mahan, Shenshen Wang, Mehran Kardar, Gur Yaari, Laura M. Walker, Birgitte B. Simen, Elizabeth P. St. John, Po-Ying Chan-Hui, Kristine Swiderek, Steven H. Kleinstein, Galit Alter, Michael S. Seaman, Arup K. Chakraborty, Daphne Koller, Ian A. Wilson, George M. Church, Dennis R. Burton and Pascal Poignard. The Effects of Somatic Hypermutation on Neutralization and Binding in the PGT121 Family of Broadly Neutralizing HIV Antibodies, PLoS Pathogens 9(11): e1003754.
  • Gur Yaari, Jason Vander Heiden, Mohamed Uduman, Daniel Gadala-Maria, Namita Gupta, Joel N.H. Stern, Kevin O’Connor, David Hafler, Uri Laserson, Francois Vigneault and Steven Kleinstein. Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput Immunoglobulin sequencing data, Frontiers in Immunology, 4(358).
  • Gur Yaari, Christopher R. Bolen, Juillee Thakar and Steven H. Kleinstein, Quantitative Set Analysis for Gene Expression: A method to quantify gene set differential expression including gene-gene correlations, Nucleic Acids Research, 41(18): e170.
  • • Liangjuan Fang, Daniel E. Lowther, Matt L. Meizlish, Jae-Yun Lee, Joel N.H. Stern, Richard C.E. Anderson, Jeffrey N. Bruce, Anita J. Huttner, Gur Yaari, Steven H. Kleinstein, Lesley Devine, Katharine M. Cronk, Laura Lovato and Kevin C. O’Connor, The immune cell infiltrate populating meningiomas is comprised of mature, antigen-experienced T and B cells, Neuro-Oncology, 15(11): 1479.
  • Luis Querol, Pamela L. Clark, Anne H. Cross, Jae-Yun Lee, Steven H. Kleinstein, Gur Yaari, David A. Hafler, Simon N. Willis and Kevin C. OConnor , Protein array-based autoantibody profiling of cerebrospinal fluid from patients with multiple sclerosis, Neurology , 81(11): 956.
  • Jamie L. Duke, Man Liu, Gur Yaari, Ashraf M. Khalil, Mary M. Tomayko, Mark J. Shlomchik, David G. Schatz and Steven H. Kleinstein, Multiple Transcription Factor Binding Sites Predict AID Targeting in Non-Ig Genes,The Journal of Immunology, 190(8): 3878.

2012

  • Gur Yaari, Mohamed Uduman and Steven H. Kleinstein,Quantifying selection in high-throughput Immunoglobulin sequencing datasets, Nucleic Acids Research, 40(17): e134.
  • Gur Yaari and Gil David, "Hot hand" on strike: Bowling data show correlation to recent past results, not causality, PLoS ONE, 7(1): e30112.
  • Gur Yaari ,Yossi Ben-Zion, Nadav M. Shnerb and David A. Vasseur, Consistent scaling of persistence time in metapopulations, Ecology, 93: 1214.

2011

  • Gur Yaari and Shmuel Eisenmann,The Hot (invisible?) Hand: can time sequence patterns of success/failure in sports be modeled as repeated random independent trials? PLoS ONE, 6(10): e24532.
  • Mohamed Uduman*, Gur Yaari*, Uri Hershberg, Mark J. Shlomchik and Steven H. Kleinstein, Detecting selection in Immunoglobulin sequences, Nucleic Acids Research, 39: 499.
  • Steven M. Kerfoot, Gur Yaari, Jaymin R. Patel, Kody L. Johnson, David G. Gonzalez, Steven H. Kleinstein and Ann M. Haberman, Inter-follicular germinal center B cell and T follicular helper cell development precedes follicular Tfh maintenance, Immunity, 34(6): 947
  • Yosi Maruvka, Gur Yaari, Sorin Solomon, David Kessler and Nadav Shnerb, Slicing and Dicing the Genome: A Statistical Physics Approach to Population Genetics, Journal of Statistical Physics, 142(6): 1302.

2010

  • Gur Yaari and Sorin Solomon, Cooperation Evolution in Random Multiplicative Environments, European Physical Journal B, 73(4): 625.
  • Yosi Ben Zion, Gur Yaari and Nadav Shnerb, Optimizing metapopulation sustainability through a checkerboard strategy, PLoS Computational Biology, 6(1): e1000643.

2009

  • Yaniv Dover, Sonia Moulet, Sorin Solomon and Gur Yaari, Do all economies grow equally fast? Risk and Decision Analysis, 1(3): 171.
  • Damien Challet and Sorin Solomon and Gur Yaari, The Universal Shape of Economic Recession and Recovery after a Shock, Economics: The Open-Access, Open-Assessment E-Journal, 3.

2008

  • Gur Yaari, Andrzej Nowak, Kamil Rakocy and Sorin Solomon, Microscopic Study Reveals the Singular Origins of Economic Growth, European Physical Journal B, 62:505.
  • Gur Yaari, Sorin Solomon, Marcelo Schiffer and Nadav M. Shnerb, Local enrichment and its nonlocal consequences for victim-exploiter meta populations, Physica D, 237(20): 2553.
  • Gur Yaari, Dietrich Stauffer and Sorin Solomon,Intermittency and Localization, Encyclopedia of Complexity and System Science, 9: 4920, Springer New York.

2006

  • Gur Yaari, Sorin Solomon and Christophe Deissenberg, Advertising, Negative Word-of-Mouth, and Product Acceptance, European Journal of Economic and Social Systems, 19(2): 257.

2005

  • Friedman, E., Bauer, M., Breitschopf, J., Clement, H., Denz, H., Doroshkevich, E., Erhardt, A., Hofman, G. J., Kritchman, S., Meier, R., Wagner, G. J. and Yaari, G., Elastic scattering of low energy pions by nuclei and the in-medium isovector pi N amplitude, Physical Review C, 72(3): 034609.

2004

  • Friedman, E., Bauer, M., Breitschopf, J., Clement, H., Denz, H., Doroshkevich, E., Erhardt, A., Hofman, G. J., Meier, R., Wagner, G. J. and Yaari, G., The in-medium isovector pi N amplitude from low energy pion scattering, Physical Review Letters, 93(12): 122302.

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